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The film begins with a back story of how black culture's popularity with the American public began to decline in the 1980s, when style and originality began to lose appeal in the public eye due to the persistent efforts of "The Man" (Robert Trumbull), a powerful Caucasian man in control of a secret organization that seeks to undermine the African-American community as well as the cultures of other minorities. The Man is infuriated that Gen. Warren Boutwell (Billy Dee Williams), a U.S. Army general based on Colin Powell, is considering running for president, and his lackey Mr. Feather (Chris Kattan) informs him of a mind control drug which The Man uses to make Boutwell abort his plans and instead open a fried chicken franchise. The B.R.O.T.H.E.R.H.O.O.D., a secret organization that battles The Man's influence, determines The Man is behind Boutwell's change of heart, and recruits a freelance agent named Undercover Brother (Eddie Griffin) to aid them.

Undercover Brother joins B.R.O.T.H.E.R.H.O.O.D. which is made up of the Chief (Chi McBride), Conspiracy Brother (Dave Chappelle), Smart Brother (Gary Anthony Williams), Sistah Girl (Aunjanue Ellis), and Lance (Neil Patrick Harris), an intern who is the only white man in the organization due to affirmative action. Undercover Brother goes undercover as a new employee at a cigarette company owned by The Man, where Mr. Feather discovers his identity. He deploys a secret weapon that he calls "Black Man's Kryptonite", an attractive assassin named White She-Devil (Denise Richards). Posing as another new employee, she and Undercover Brother start dating, and she begins to make him do stereotypical "white" things, such as buying corduroy and khaki clothes, singing karaoke, and adopting a silly set of euphemisms. Meanwhile, The Man distributes his mind control drug through Boutwell's fried chicken, infecting other black celebrities and making them act white.

Concerned with Undercover Brother's unusual behavior, Sistah Girl attacks White She-Devil and convinces Undercover Brother to return to the fight. White-She-Devil turns on her own henchmen to save the two, revealing she has fallen in love with Undercover Brother. They return to the B.R.O.T.H.E.R.H.O.O.D., where Smart Brother questions White She-Devil about The Man and Lance is officially made part of the group when he declares his desire to abolish bigotry after watching Roots. The group heads to an awards gala after they find out that James Brown is The Man's next target. Mr. Feather kidnaps Brown and takes him to The Man's base. B.R.O.T.H.E.R.H.O.O.D. secures an antidote for the mind control drug and follows via a transmitter placed on Brown, infiltrating the base posing as a cleaning crew, to rescue Brown and a mysterious "Candidate" that The Man plans to use to land a crushing blow to black culture.

Mr. Feather prepares to administer the drug to Brown and present him as a trophy to The Man, and Brown reveals himself as Undercover Brother in disguise. Mr. Feather sends his henchmen after B.R.O.T.H.E.R.H.O.O.D., who discover the Candidate is Boutwell, and is ordered by Mr. Feather to kill Undercover Brother. In the fighting, Conspiracy Brother accidentally begins the building's self-destruct sequence. The B.R.O.T.H.E.R.H.O.O.D. cures Boutwell and evacuate him from the building while Undercover Brother chases Mr. Feather to the roof. The Man's helicopter circles overhead and leaves, The Man abandoning Mr. Feather for failing him. Mr. Feather jumps onto the helicopter's landing gear as it flies away, and Undercover Brother uses his afro picks to impale Mr. Feather in the buttocks, causing him to fall into the ocean, where he is eaten by a shark. However, The Man escapes. Undercover Brother survives the building's self-destruct by leaping off the building and using his wide pants legs as parachutes. He and Sistah Girl kiss and leave the island, the world at peace.

The film holds a 77% rating on Rotten Tomatoes based on 130 reviews, with the critics consensus: Fast-paced and filled with racial gags, Undercover Brother serves up plenty of laughs and sharp satire.[2] On Metacritic, the film received a 69% rating based on 30 reviews, indicating "Generally favorable reviews".[3]